Through-fastened deck boards look a lot better if the fastenings are in line and at uniform spacing to the edges of the boards. Pre-drilling deck boards is a good idea in any case, if you are fastening tropical hardwood, it’s an absolute must.
For a deck project with 20mm x 100mm (3/4’’ x 4’’) Brazilian walnut boards, I made a simple drilling template out of an 12’’ long cutoff from one of the deck boards and a pair of 3’’ zinc plated corner braces. The corner braces are spaced to exactly fit the sleepers to which the boards are fastened. I attached an old cabinet handle to make the template easier to place and pickup.
In making the template, I marked the exact location of the holes and then drilled them on my drill press so they’d be perfectly plumb. The holes get bigger along with the number of drillings. After some 1000 drillings, my 6mm diameter holes had become 7 mm diameter holes, however, this didn’t seem to significantly affect the accurate location and plumb of the holes I was drilling.
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